APPENDIX B Sequence and Analysis of Polyoma Virus DNA

Abstract

The polyoma virus A-2 (large-plaque) strain contains 5292 base pairs. The following analysis is based on the DNA sequence of this strain, as determined by Soeda et al. (1980), and on other data presented in the references cited below. The sequence and data presented in this appendix are intended not as a definitive work on polyoma virus, but as a guide for those interested in the study of this small DNA tumor virus. Six proteins have been identified to date as being encoded within the viral DNA; they have been designated large, middle, and small T antigens (the so-called early proteins) and VP1, VP2, and VP3 (the late or viral capsid proteins). The DNA sequence suggests that there could be other, as yet undiscovered, viral proteins. For example, within the early region of the sequence, from nucleotides between positions 2584 and 2874, a small polypeptide of just less than 100 amino acids could be produced. Moreover, a judicious choice of splicing sites in the viral mRNAs could either create messengers capable of producing proteins other than those described here or, alternatively, create sequence microheterogeneity within the known proteins, which in itself could lead to functional alterations. By such means, the virus could essentially expand its coding capacity. Other strains of polyoma virus may have a slightly different DNA sequence. For example, it is already known that the A-3 (large-plaque) strain is missing 11 bp found in the A-2 strain sequence between positions 44 and 54 (see Section 1). The Physical...